Contacts of the helix formed by residues 85 - 99 (chain A) in PDB entry 1JS6
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 85 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A SER* 1.3 76.7 + - - +
86A TYR* 1.3 65.2 + - - +
87A PRO* 3.4 9.7 - - - +
88A ALA* 3.2 14.0 + - - +
89A MET* 3.1 26.9 + - - +
306A LEU* 2.9 31.1 + - - +
308A ASN* 3.0 7.6 + - - +
365A VAL* 3.8 5.5 - - - +
369A TYR* 3.7 17.9 - - - -
453A ARG* 4.5 5.4 - - - +
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Residues in contact with TYR 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA* 4.9 2.3 - - - -
21A LEU* 3.6 30.2 - - + +
85A SER* 1.3 71.4 - - - +
87A PRO* 1.3 70.6 - - + +
89A MET* 3.1 21.7 + - + +
90A LEU* 2.9 29.8 + - - +
369A TYR* 5.0 1.0 + - - -
453A ARG* 3.5 25.1 + - - -
454A LYS* 3.8 4.3 + - - -
1B MET* 3.5 39.3 - - + -
2B ASN* 3.4 22.7 - - - -
3B ALA* 3.5 22.5 + - - +
6B PHE* 3.1 44.1 - + + -
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Residues in contact with PRO 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A SER* 3.4 13.2 - - - +
86A TYR* 1.3 96.0 - - + +
88A ALA* 1.3 61.1 + - - +
90A LEU* 3.4 1.2 + - + +
91A ALA 3.0 17.7 + - - -
364A PHE* 3.4 39.1 - - - +
365A VAL* 4.0 5.8 - - - -
368A MET* 3.8 34.8 - - + -
369A TYR* 3.6 20.9 - - + +
1B MET* 4.3 12.6 - - + +
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A SER* 3.2 11.5 + - - +
87A PRO* 1.3 74.7 - - - +
89A MET* 1.3 55.8 + - - +
91A ALA* 3.1 8.8 + - - +
92A ASP* 2.6 36.9 + - - +
307A VAL* 4.3 1.1 - - - -
308A ASN* 3.1 42.8 - - + +
361A LYS* 3.8 12.4 - - + +
365A VAL* 3.8 16.0 - - + +
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Residues in contact with MET 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A MET* 3.9 26.9 - - + -
21A LEU* 4.9 9.2 - - + -
84A SER* 3.5 24.7 - - - +
85A SER 3.1 23.4 + - - +
86A TYR* 3.1 32.7 + - + +
88A ALA* 1.3 75.1 - - - +
90A LEU* 1.3 66.1 + - - +
92A ASP* 3.1 8.3 + - - +
93A MET* 3.0 28.6 + - - +
308A ASN* 3.5 15.7 - - - +
453A ARG* 5.8 2.5 - - - +
6B PHE* 4.4 8.1 - - + -
96B GLY* 4.2 14.8 - - - +
97B ALA* 4.2 9.6 - - - -
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TYR 2.9 21.4 + - - +
87A PRO* 3.6 4.9 - - + +
88A ALA 3.3 0.2 - - - -
89A MET* 1.3 76.0 - - - +
91A ALA* 1.3 63.8 + - - +
93A MET* 3.1 21.4 + - - +
94A LEU 3.2 9.5 + - - -
364A PHE* 4.2 11.0 - - + -
368A MET* 3.4 31.4 - - + -
1B MET* 4.4 11.4 - - - -
6B PHE* 3.9 11.0 - - + -
9B ARG* 3.9 11.2 - - + +
10B GLY* 3.6 36.3 - - - +
13B MET* 3.8 21.1 - - + +
53B PHE* 3.9 11.9 - - + -
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A PRO 3.0 13.8 + - - +
88A ALA 3.3 8.5 - - - +
90A LEU* 1.3 76.7 - - - +
92A ASP* 1.3 63.2 + - - +
94A LEU* 3.1 5.4 + - - +
95A CYS* 2.9 23.8 + - - +
360A LEU* 3.5 30.6 - - + +
361A LYS* 3.6 14.8 - - - -
364A PHE* 3.5 20.4 - - + -
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Residues in contact with ASP 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ALA 2.6 19.4 + - - +
89A MET* 3.1 8.9 + - - +
91A ALA* 1.3 72.2 - - - +
93A MET* 1.3 63.5 + - - +
95A CYS* 3.2 8.9 + - - +
96A GLY* 3.0 20.6 + - - -
308A ASN* 5.5 3.5 - - + +
356A ARG* 3.5 24.1 + - - -
361A LYS* 3.1 29.6 + - + +
92B ASP* 2.8 27.8 - - - +
356B ARG* 4.3 3.6 + - - -
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Residues in contact with MET 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 4.7 0.2 - - + -
17A MET* 5.4 2.2 - - + -
89A MET 3.0 20.3 + - - +
90A LEU* 3.1 15.7 + - - +
92A ASP* 1.3 78.7 - - - +
94A LEU* 1.3 61.6 + - - +
96A GLY* 3.3 2.3 + - - -
97A ALA* 3.1 16.6 + - - +
6B PHE* 4.9 9.6 - - - -
10B GLY* 3.9 8.3 - - - +
13B MET* 3.9 15.0 - - + -
14B VAL* 3.5 25.6 - - + -
17B MET* 3.4 37.1 - - + +
89B MET* 5.9 0.2 - - - +
93B MET* 3.5 51.8 - - + -
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU 3.2 6.9 + - - +
91A ALA* 3.1 8.6 + - - +
93A MET* 1.3 79.0 - - - +
95A CYS* 1.3 56.3 + - - +
97A ALA* 2.8 30.4 + - + +
98A ILE* 2.9 35.3 + - + +
360A LEU* 4.1 16.6 - - + -
364A PHE* 3.8 24.5 - - + -
13B MET* 4.2 14.3 - - + -
16B TYR* 3.6 33.7 - - + -
17B MET* 4.8 0.9 - - + -
20B TYR* 6.4 1.1 - - + -
57B LEU* 5.4 0.2 - - + -
60B VAL* 3.8 25.4 - - + -
65B MET* 5.2 0.7 - - + -
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Residues in contact with CYS 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ALA 2.9 12.4 + - - +
92A ASP* 3.3 15.5 - - - +
94A LEU* 1.3 75.5 - - - +
96A GLY* 1.3 58.2 + - - +
98A ILE* 3.6 4.1 + - - +
99A GLY* 2.9 25.8 + - - -
100A CYS 4.6 0.9 + - - -
356A ARG* 4.0 26.2 - - - -
357A PHE* 3.5 44.5 - - - +
358A ARG* 4.9 1.8 - - - -
360A LEU* 3.7 17.0 - - + +
361A LYS* 6.0 1.6 - - + -
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Residues in contact with GLY 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ASP 3.0 14.0 + - - -
93A MET* 3.7 4.0 - - - -
95A CYS* 1.3 78.3 - - - +
97A ALA* 1.3 62.1 + - - +
99A GLY* 3.4 11.9 + - - -
356A ARG* 6.0 0.4 - - - +
84B SER* 4.2 4.3 + - - -
89B MET* 4.2 8.0 - - - +
308B ASN* 3.6 26.7 + - - -
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Residues in contact with ALA 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A MET 3.1 12.2 + - - +
94A LEU* 2.8 19.0 + - + +
96A GLY* 1.3 69.9 - - - +
98A ILE* 1.3 66.1 + - - +
99A GLY* 3.1 1.2 + - - -
17B MET* 3.7 28.0 - - + -
20B TYR* 3.7 16.3 - - + -
21B LEU* 3.9 26.9 - - + +
72B HIS* 4.2 5.4 - - - -
84B SER* 4.7 1.9 + - - -
89B MET* 4.2 10.2 - - - -
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Residues in contact with ILE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A LEU* 2.9 43.1 + - + +
95A CYS* 4.0 3.4 - - - +
97A ALA* 1.3 75.6 - - - +
99A GLY* 1.3 65.3 + - - +
100A CYS* 3.3 21.6 + - + +
357A PHE* 4.4 22.7 - - + -
360A LEU* 4.5 3.8 - - + -
20B TYR* 3.9 17.3 + - + +
60B VAL* 5.2 1.3 - - + -
64B ILE* 4.8 6.1 - - + -
65B MET* 4.3 22.2 - - + -
68B VAL* 3.8 35.0 - - + -
69B THR 5.5 0.3 - - - +
70B HIS* 5.7 0.3 - - - -
71B TRP 5.1 4.0 + - - -
72B HIS* 3.4 11.4 - - - -
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Residues in contact with GLY 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A CYS 2.9 18.4 + - - -
96A GLY* 3.6 12.1 - - - -
97A ALA 3.1 1.8 - - - -
98A ILE* 1.3 76.6 - - - +
100A CYS* 1.3 59.6 + - - +
101A ILE* 5.5 0.9 - - - -
71B TRP* 3.9 1.6 - - - +
72B HIS* 2.9 26.8 + - - -
82B THR* 3.4 14.0 - - - +
83B ALA 5.2 2.0 - - - +
84B SER* 5.6 0.9 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il